Unfortunately, the DEPARTMENT OF DEFENSE GOVERNMENT CHARGE CARD GUIDEBOOK FOR ESTABLISHING AND MANAGING PURCHASE, TRAVEL, AND FUEL CARD PROGRAMS provides no relief or instructions for this type of scenario.
Reminder, it's the total value of the action and not just the cost/price of the labor that must be below $2,500 for SCLS not to apply (I've answered that question a few times here at AAP).
If you are the cardholder and the repair service has not been accomplished yet, take this action to your Contracting Office with a purchase request and they should be able to issue a purchase order that has the appropriate Service Contract Labor Standards (SLCS) clause to have the repair done. Should be simple as that.
However, if the repair work has been completed and the card charged; again speak with your contracting office and chain of command for how your organization reports these violations.
If the service has been completed but not yet been paid for (they have not charged the card) and accepted, you may have a couple of options:
1) Look at FAR 22.1003-4(d) in its entirety. You'll see "Automobile or other vehicle (e.g., aircraft) maintenance services..." at FAR 22.1003-4(d)(1)(i). It's a long shot but maybe all of the facts of the scenario may uncover you have an exemption here. Again, a long shot but worth the analysis.
2) Go down the ratification path and if it is chosen to be ratified, the resultant purchase order would include the applicable SCLS clause.